Dockerfile.jammy

FROM ubuntu:jammy

# Configure apt-get to use the mirror in us-east-1 instead of the Docker default of archive.ubuntu.com
RUN sed -i "s/archive.ubuntu.com/us-east-1.ec2.archive.ubuntu.com/g" /etc/apt/sources.list

# update apt & install packages
RUN apt-get update -qq && \
    DEBIAN_FRONTEND=noninteractive apt-get install -y \
    build-essential \
    cmake \
    curl \
    git \
    gnupg \
    libboost-all-dev \
    libcurl4-openssl-dev \
    locales \
    lsb-release \
    openssh-client \
    protobuf-compiler \
    sudo && \
    rm -rf /var/lib/apt/lists/*

# add R apt repository
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 0x51716619e084dab9 && \
    echo "deb http://cran.rstudio.com/bin/linux/ubuntu jammy-cran40/" >> /etc/apt/sources.list.d/cran-rstudio.list

# Ensure FreeTDS is added to unixodbc upon installation
RUN echo tdsodbc freetds/addtoodbc boolean true | debconf-set-selections

# Install libraries & database related packages separately to break up the layers
RUN apt-get update -qq && \
    DEBIAN_FRONTEND=noninteractive apt-get install -y \
    gdebi-core \
    jags \
    libaio1 \
    libatlas3-base \
    libcairo2 \
    libcairo2-dev \
    libev-dev \
    libfftw3-dev \
    libgdal-dev \
    libgraphviz-dev \
    libgsl0-dev \
    libmagick++-dev \
    libmysqlclient21 \
    libmysqlclient-dev \
    libnetcdf-dev \
    libpcre2-dev \
    libprocps-dev \
    libproj-dev \
    libprotoc-dev \
    libquantlib0-dev \
    libsasl2-dev \
    libssh-dev \
    libsqliteodbc \
    libxml2-dev \
    libxt-dev \
    libxt6 \
    odbc-postgresql \
    tdsodbc \
    unixodbc \
    unixodbc-dev \
    wget \
    zip && \
    rm -f /etc/ImageMagick-6/policy.xml && \
    rm -rf /var/lib/apt/lists/*

# Install the RStudio Professional Drivers (includes mysql drivers)
RUN wget -q https://cdn.rstudio.com/drivers/7C152C12/installer/rstudio-drivers_2023.05.0_amd64.deb && \
    gdebi -n rstudio-drivers_2023.05.0_amd64.deb && \
    cat /opt/rstudio-drivers/odbcinst.ini.sample >> /etc/odbcinst.ini  && \
    rm rstudio-drivers_2023.05.0_amd64.deb

# Install JDK and Cargo separately to avoid the recommended packages
RUN apt-get update -qq && \
    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends openjdk-11-jdk cargo && \
    rm -rf /var/lib/apt/lists/*

RUN apt-get update -qq && \
    DEBIAN_FRONTEND=noninteractive apt-get install -y \
    python3-dev \
    python3-pip \
    python3-venv \
    python3-virtualenv && \
    rm -rf /var/lib/apt/lists/*

# Install Julia
RUN wget -q https://julialang-s3.julialang.org/bin/linux/x64/1.9/julia-1.9.1-linux-x86_64.tar.gz && \
    tar -C /usr/local -zxf julia-1.9.1-linux-x86_64.tar.gz && \
    ln -s /usr/local/julia-1.9.1/bin/julia /usr/local/bin/julia && \
    rm julia-1.9.1-linux-x86_64.tar.gz

# Install of texlive. Use --no-install-recommends to avoid installing ~750MB of documentation
RUN apt-get update -qq && \
    DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \
    texlive-full && \
    rm -rf /var/lib/apt/lists/*


# add in the less secure openssl config file
# End-user applications can optionally reference this file to allow connection to less secure systems.
# https://community.rstudio.com/t/rmysql-to-mysql-database-on-aws-ssl-connection-error-after-deploying/100676
COPY insecure-openssl.cnf /etc/ssl/insecure-openssl.cnf

RUN apt-get update -qq && \
    DEBIAN_FRONTEND=noninteractive TZ='Etc/UTC' apt-get install tzdata && \
    apt-get install -s r-base-core r-base-dev | sed -e "/The following additional packages will be installed/,/^\w/!d;//d" -e "s/\br-.*\b//g" | xargs apt-get install -y

# set default locale
RUN update-locale --reset LANG=C.UTF-8

# set a non-default global location for Renviron.site.
# This would typically be found at $R_HOME/etc/Renviron.site, but we'd like it not to be a layer in the per-R version images.
# https://stat.ethz.ch/R-manual/R-devel/library/base/html/Startup.html
ENV R_ENVIRON /etc/R/Renviron.site
COPY Renviron.site /etc/R/Renviron.site

ARG R_VERSION=4.3.1

ENV PATH /opt/R/${R_VERSION}/bin:$PATH

# Install R
RUN wget -q https://cdn.rstudio.com/r/ubuntu-2204/R-${R_VERSION}-ubuntu-2204.tar.gz -O /tmp/R-${R_VERSION}.tar.gz && \
    mkdir -p /opt/R && \
    tar zx -C /opt/R -f /tmp/R-${R_VERSION}.tar.gz && \
    rm /tmp/R-${R_VERSION}.tar.gz